Python environment

It is always recommended to install BacterialTyper and all its dependencies and modules under a python environment.

Take into account that you might need to have installed several developer libraries in your system. See section System requirements for details.

By executing the env/create_python_environment.sh script, it creates an environment, installs all python requirements and activates it for later usage.

You only have to create the environment once and you can populate with additional modules, see details in Install modules.

Make sure to deactivate the environment after finishing the exection of `BacterialTyper or activate it before running it, following the instructions in Deactivate environment or Activate environment sections respectively.

Create environment

To do so, run env/create_python_environment.sh, which is shown below:

#!/usr/bin/env bash

echo ""
echo ""
echo "##### Create a virtual environment for BacterialTyper ####"
echo ""

export PYTHONPATH=""
echo "python3 -m venv env/BacterialTyper"
python3 -m venv env/BacterialTyper
echo "Done..."
echo ""

echo "#### Activate virtual environment ####"
echo "source env/BacterialTyper/bin/activate"
source env/BacterialTyper/bin/activate
echo "Done..."
echo ""

## upgrade pip
echo "#### Upgrade pip package installer ####"
echo "pip install -I --isolated --upgrade pip"
pip install -I --isolated --upgrade pip
echo "Done...."
echo ""

# install BacterialTyper requirements

echo "#### Install pip package requirements ####"
echo "pip install -I --isolated --default-timeout=500 -r BacterialTyper/config/python/min_python_requirements.txt"
pip install -I --isolated --default-timeout=500 -r BacterialTyper/config/python/min_python_requirements.txt
echo "Done...."
echo ""

echo "Exit...."
echo ""

Execute the file from the main directory as:

source env/create_python_environment.sh

Within this create environment script, there is a command to install all python requirements for BacterialTyper:

pip install -r BacterialTyper/config/python_requirements.txt

Activate environemt

Before executing any BacterialTyper module or script, it is convenient to activate the environment.

To do so, run env/activate_environment.sh, which is shown below:

#!/usr/bin/env bash

echo ""
echo ""
echo "##### Activate the virtual environment for BacterialTyper ####"
echo ""

DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
echo "source $DIR/BacterialTyper/bin/activate"
source $DIR/BacterialTyper/bin/activate
echo "Done..."
echo ""

echo "Exit...."
echo ""

Execute the file from the directory BacterialTyper/ as:

source env/activate_environment.sh

Deactivate environemt

After finished the execution of any BacterialTyper module or script, it is convenient to deactivate the environment. You can just close the terminal but it would be more appopiate to conveniently deactivate the environment first.

To do so, execute the following command:

deactivate

Install modules

Once the BacterialTyper environment is created, install using pip BacterialTyper or any additional modules.

e.g.: Install BacterialTyper

python -m pip install BacterialTyper

e.g.: install a list of requirements

pip install -r BacterialTyper/config/python_requirements.txt

Attention

Installing BacterialTyper using pip installs all the python requirements. For additional third-party software and software required for BacterialTyper to work you will need to run the config module.